Contacts of the helix formed by residues 104 - 122 (chain A) in PDB entry 2Q8F
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ASN 3.3 20.6 + - - +
101A LEU* 2.9 17.5 + - - +
103A ARG* 1.3 79.4 - - - +
105A PRO* 1.3 63.7 - - - +
107A VAL* 3.2 20.8 + - - +
108A GLN* 3.0 27.2 + - - +
159A GLY* 3.5 19.4 - - - +
162A GLU* 3.2 29.0 + - + -
163A TYR* 3.7 8.5 - - - +
167A PHE* 5.3 2.5 - - + -
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Residues in contact with PRO 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG 3.6 2.9 - - - +
104A THR* 1.3 84.6 - - + +
106A SER* 1.3 54.7 + - - +
108A GLN* 3.8 7.2 - - + +
109A LEU* 2.9 29.1 + - - +
162A GLU* 3.2 26.2 - - + +
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PRO* 1.3 74.5 - - - +
107A VAL* 1.3 63.9 + - - +
109A LEU* 3.3 5.6 + - - +
110A VAL* 3.1 27.4 + - - +
155A THR* 3.1 34.6 - - - +
158A GLN* 3.5 11.1 - - - +
159A GLY* 3.4 9.6 - - - -
162A GLU* 2.6 33.4 + - - -
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ILE* 4.4 7.4 - - + -
97A LEU* 4.2 13.2 - - + -
101A LEU* 3.4 27.8 - - + +
102A LEU* 3.8 33.2 - - + +
104A THR* 3.2 21.6 + - - +
106A SER* 1.3 72.6 - - - +
108A GLN* 1.3 61.1 + - - +
110A VAL* 3.3 6.5 + - - +
111A GLN* 2.9 27.7 + - - +
156A MET* 4.0 25.8 - - + -
159A GLY* 4.0 7.0 - - - -
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Residues in contact with GLN 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 2.7 34.9 + - - +
103A ARG* 4.0 13.3 - - - +
104A THR 3.0 21.8 + - - +
105A PRO* 3.8 7.4 - - + +
107A VAL* 1.3 77.4 - - - +
109A LEU* 1.3 57.3 + - - +
111A GLN* 3.6 25.8 + - - +
112A SER* 2.9 29.3 + - - -
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PRO 2.9 18.7 + - - +
106A SER* 3.6 5.8 - - - +
107A VAL 3.2 0.2 - - - -
108A GLN* 1.3 74.8 - - - +
110A VAL* 1.3 65.1 + - - +
112A SER* 2.7 25.1 + - - +
113A TRP* 3.0 51.4 + - + +
155A THR* 4.2 11.7 - - + -
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ILE* 4.9 3.1 - - + -
106A SER 3.1 15.8 + - - +
107A VAL* 3.7 8.5 - - - +
109A LEU* 1.3 73.8 - - - +
111A GLN* 1.3 65.6 + - - +
113A TRP* 3.1 18.1 + - + +
114A TYR* 3.0 35.2 + - + -
152A VAL* 4.3 8.1 - - + +
155A THR* 3.7 24.9 - - + -
156A MET* 4.0 22.9 - - + +
184A PHE* 3.8 30.1 - - + -
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Residues in contact with GLN 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET* 5.1 5.5 + - + +
94A ILE* 3.6 36.7 - - + +
95A SER* 4.2 14.3 + - - +
102A LEU* 4.1 9.7 - - - +
107A VAL* 2.9 17.7 + - + +
108A GLN* 3.7 28.4 + - - +
110A VAL* 1.3 78.5 - - - +
112A SER* 1.3 56.4 + - - +
114A TYR* 3.3 7.9 + - + +
115A ILE* 3.0 47.3 + - + +
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Residues in contact with SER 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLN 2.9 17.2 + - - -
109A LEU* 2.7 30.9 + - - +
111A GLN* 1.3 71.6 - - - +
113A TRP* 1.3 68.0 + - - +
115A ILE* 3.4 10.6 + - - +
116A GLN* 3.0 25.3 + - - +
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Residues in contact with TRP 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 3.0 49.1 + - + +
110A VAL* 3.1 18.1 + - + +
112A SER* 1.3 80.8 + - - +
114A TYR* 1.3 57.7 + - + +
116A GLN* 3.3 5.0 + - - +
117A SER* 2.9 34.3 + - - -
148A ARG* 3.7 43.4 - - + +
149A HIS* 3.7 15.7 - - + +
151A ASP* 4.3 8.5 - - + -
152A VAL* 3.7 36.8 - - + -
155A THR* 3.8 26.2 - - + -
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Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 3.5 25.3 - - + +
90A ILE* 3.6 25.0 - - + +
91A MET* 3.9 31.8 - - + +
94A ILE* 4.6 6.3 - - + -
110A VAL* 3.0 33.1 + - + +
111A GLN* 3.3 9.6 + - + +
113A TRP* 1.3 77.0 - - + +
115A ILE* 1.3 57.8 + - - +
117A SER* 3.8 1.1 - - - -
118A LEU* 2.9 31.7 + - - +
149A HIS* 3.5 30.6 + + - -
152A VAL* 4.1 9.0 - - + +
184A PHE* 3.6 23.2 - + - -
187A SER* 5.1 0.3 + - - -
188A ARG* 4.0 24.1 + - - +
191A ILE* 4.4 6.4 - - + +
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Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 4.0 30.7 - - + -
91A MET* 3.7 22.4 - - + -
111A GLN* 3.0 43.2 + - + +
112A SER* 3.7 8.5 - - - +
113A TRP 3.3 0.2 - - - -
114A TYR* 1.3 74.9 - - - +
116A GLN* 1.3 58.5 + - - +
118A LEU* 3.6 2.8 + - - +
119A GLN* 3.0 48.4 + - - +
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER 3.0 17.4 + - - +
113A TRP* 3.8 6.2 - - - +
114A TYR 3.3 0.2 - - - -
115A ILE* 1.3 75.5 - - - +
117A SER* 1.3 58.9 + - - +
119A GLN* 3.3 12.1 + - - +
120A GLU* 3.0 47.2 + - + +
148A ARG* 3.4 30.7 + - - +
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 4.1 9.4 - - - -
113A TRP 2.9 9.8 + - - -
114A TYR 3.9 3.1 - - - -
116A GLN* 1.3 73.2 - - - +
118A LEU* 1.3 65.2 + - - +
120A GLU* 3.3 2.8 + - - +
121A LEU* 3.0 27.9 + - - +
145A ILE* 3.7 23.0 - - - +
148A ARG* 3.2 19.5 + - - +
149A HIS* 2.7 34.1 + - - -
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 5.1 2.5 - - + +
45A GLN* 4.4 12.3 - - + +
46A VAL* 3.6 41.7 - - + +
49A TYR* 4.9 1.8 - - + -
84A PRO* 3.7 42.8 - - + +
87A LEU* 3.8 12.8 - - + +
88A ALA* 4.8 4.0 - - + +
91A MET* 4.0 15.5 - - + -
114A TYR 2.9 21.6 + - - +
115A ILE 3.7 4.7 - - - +
116A GLN 3.4 0.2 - - - -
117A SER* 1.3 74.1 - - - +
119A GLN* 1.3 62.8 + - + +
121A LEU* 3.2 2.7 + - - +
122A LEU* 3.0 39.4 + - + +
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Residues in contact with GLN 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 3.3 28.4 - - + +
45A GLN* 4.0 20.2 + - - +
115A ILE* 3.0 32.6 + - + +
116A GLN* 3.7 10.9 - - - +
118A LEU* 1.3 76.0 - - + +
120A GLU* 1.3 63.5 + - + +
122A LEU* 3.4 14.8 + - - +
123A ASP* 3.4 20.6 + - - +
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLN* 3.0 29.2 + - + +
117A SER 3.3 4.2 + - - +
119A GLN* 1.3 75.2 - - + +
121A LEU* 1.3 62.1 + - - +
123A ASP* 3.4 16.6 + - - +
124A PHE* 3.3 21.8 - - - -
141A THR* 3.9 14.6 - - + -
144A ARG* 3.3 27.8 + - - +
145A ILE* 4.1 6.1 - - - +
148A ARG* 2.9 44.0 + - - -
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Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 4.8 6.9 - - - +
83A LEU* 3.7 31.9 - - + -
84A PRO* 4.1 16.6 - - + -
87A LEU* 3.7 25.4 - - + -
117A SER 3.0 21.5 + - - +
118A LEU* 3.7 4.9 - - - +
120A GLU* 1.3 77.7 - - - +
122A LEU* 1.3 58.9 + - - +
123A ASP 3.1 5.6 + - - -
124A PHE* 3.2 22.7 + - - +
125A LYS* 4.3 1.6 + - - +
138A PHE* 3.7 33.6 - - + -
141A THR* 4.5 6.3 - - + -
142A VAL* 5.1 3.1 - - + -
145A ILE* 3.7 24.2 - - + -
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLN* 3.6 46.7 - - + +
49A TYR* 3.3 42.0 - - + +
80A ARG 5.2 1.1 - - - +
84A PRO* 3.8 20.6 - - + -
118A LEU* 3.0 32.6 + - + +
119A GLN* 3.8 7.6 - - - +
120A GLU 3.3 0.4 - - - -
121A LEU* 1.3 72.0 - - - +
123A ASP* 1.3 60.9 + - - +
124A PHE 3.1 5.6 - - - -
125A LYS* 3.4 30.3 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il